Imputation Report For Cohort: Group2

Per chromosome imputation report for cohort Group2.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 31.5.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 12653691 73.298
0.1 1220307 7.069
0.2 812775 4.708
0.3 618217 3.581
0.4 497794 2.884
0.5 407021 2.358
0.6 350248 2.029
0.7 291848 1.691
0.8 244465 1.416
0.9 166909 0.967
Total 17263275 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 751881 4.355
0.4 832242 4.821
0.5 1067249 6.182
0.6 1526125 8.840
0.7 2109598 12.220
0.8 2792620 16.177
0.9 8155765 47.243
1.0 27795 0.161
Total 17263275 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 966464 73.7469
0.1 90432 6.9005
0.2 58264 4.4459
0.3 45461 3.4689
0.4 37557 2.8658
0.5 30976 2.3637
0.6 26908 2.0532
0.7 21701 1.6559
0.8 18812 1.4355
0.9 13940 1.0637
Total 1310515

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 59333 4.5275
0.4 64640 4.9324
0.5 82302 6.2801
0.6 118549 9.0460
0.7 164725 12.5695
0.8 211431 16.1334
0.9 607588 46.3625
1.0 1947 0.1486
Total 1310515

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1062986 73.9518
0.1 100913 7.0205
0.2 65457 4.5538
0.3 49636 3.4532
0.4 38709 2.6930
0.5 33285 2.3156
0.6 28755 2.0005
0.7 23487 1.6340
0.8 20060 1.3956
0.9 14116 0.9820
Total 1437404

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 61372 4.2696
0.4 67097 4.6679
0.5 86624 6.0264
0.6 124240 8.6434
0.7 174464 12.1374
0.8 234141 16.2892
0.9 687501 47.8294
1.0 1965 0.1367
Total 1437404

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 891164 73.3694
0.1 87679 7.2186
0.2 55340 4.5561
0.3 42641 3.5106
0.4 35909 2.9564
0.5 29176 2.4021
0.6 24085 1.9829
0.7 20729 1.7066
0.8 16614 1.3678
0.9 11289 0.9294
Total 1214626

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 49910 4.1091
0.4 55343 4.5564
0.5 70639 5.8157
0.6 103786 8.5447
0.7 147367 12.1327
0.8 193245 15.9098
0.9 591561 48.7031
1.0 2775 0.2285
Total 1214626

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 880054 72.6623
0.1 82339 6.7984
0.2 61750 5.0984
0.3 44561 3.6792
0.4 34022 2.8091
0.5 27985 2.3106
0.6 24660 2.0361
0.7 21829 1.8023
0.8 20015 1.6526
0.9 13941 1.1510
Total 1211156

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 49978 4.1265
0.4 54419 4.4931
0.5 70545 5.8246
0.6 100315 8.2826
0.7 143599 11.8564
0.8 193523 15.9784
0.9 596963 49.2887
1.0 1814 0.1498
Total 1211156

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 809036 73.4824
0.1 76612 6.9584
0.2 52758 4.7919
0.3 40736 3.6999
0.4 31655 2.8751
0.5 24052 2.1846
0.6 22904 2.0803
0.7 18065 1.6408
0.8 15241 1.3843
0.9 9934 0.9023
Total 1100993

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 45207 4.1060
0.4 49071 4.4570
0.5 62687 5.6937
0.6 92436 8.3957
0.7 132589 12.0427
0.8 178904 16.2493
0.9 538659 48.9248
1.0 1440 0.1308
Total 1100993

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 789120 72.6253
0.1 80089 7.3709
0.2 52697 4.8499
0.3 40869 3.7613
0.4 32865 3.0247
0.5 26260 2.4168
0.6 22717 2.0907
0.7 16931 1.5582
0.8 15154 1.3947
0.9 9861 0.9075
Total 1086563

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 41965 3.8622
0.4 45623 4.1988
0.5 58133 5.3502
0.6 84977 7.8207
0.7 120028 11.0466
0.8 164236 15.1152
0.9 568000 52.2749
1.0 3601 0.3314
Total 1086563

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 709376 72.9805
0.1 69807 7.1817
0.2 47705 4.9079
0.3 35463 3.6484
0.4 28956 2.9790
0.5 23917 2.4606
0.6 18839 1.9382
0.7 16487 1.6962
0.8 12453 1.2812
0.9 9005 0.9264
Total 972008

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 40973 4.2153
0.4 45175 4.6476
0.5 58321 6.0001
0.6 84152 8.6575
0.7 118484 12.1896
0.8 158916 16.3492
0.9 464928 47.8317
1.0 1059 0.1089
Total 972008

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 700672 73.8915
0.1 64523 6.8045
0.2 44129 4.6538
0.3 32400 3.4168
0.4 27786 2.9303
0.5 21621 2.2801
0.6 19308 2.0362
0.7 15456 1.6300
0.8 13495 1.4232
0.9 8855 0.9338
Total 948245

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 39605 4.1767
0.4 43964 4.6364
0.5 55421 5.8446
0.6 79920 8.4282
0.7 111709 11.7806
0.8 151465 15.9732
0.9 464501 48.9853
1.0 1660 0.1751
Total 948245

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 530159 73.3257
0.1 53789 7.4395
0.2 34106 4.7172
0.3 24676 3.4129
0.4 21012 2.9061
0.5 15505 2.1445
0.6 14616 2.0215
0.7 12049 1.6665
0.8 9961 1.3777
0.9 7146 0.9884
Total 723019

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 29863 4.1303
0.4 33248 4.5985
0.5 43454 6.0101
0.6 62832 8.6902
0.7 89399 12.3647
0.8 120564 16.6751
0.9 342617 47.3870
1.0 1042 0.1441
Total 723019

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 611961 72.9377
0.1 60678 7.2320
0.2 39897 4.7552
0.3 28872 3.4412
0.4 24831 2.9595
0.5 20732 2.4710
0.6 16761 1.9977
0.7 14540 1.7330
0.8 12649 1.5076
0.9 8098 0.9652
Total 839019

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 34278 4.0855
0.4 38206 4.5537
0.5 48704 5.8049
0.6 69793 8.3184
0.7 98635 11.7560
0.8 135049 16.0961
0.9 413190 49.2468
1.0 1164 0.1387
Total 839019

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 613010 73.1766
0.1 58073 6.9323
0.2 36816 4.3948
0.3 31124 3.7154
0.4 23517 2.8073
0.5 20687 2.4695
0.6 18655 2.2269
0.7 14203 1.6954
0.8 12440 1.4850
0.9 9188 1.0968
Total 837713

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 33533 4.0029
0.4 36465 4.3529
0.5 46964 5.6062
0.6 70529 8.4192
0.7 101522 12.1189
0.8 135461 16.1703
0.9 410981 49.0599
1.0 2258 0.2695
Total 837713

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 584696 73.1809
0.1 56462 7.0668
0.2 36010 4.5070
0.3 30382 3.8026
0.4 23211 2.9051
0.5 18891 2.3644
0.6 15973 1.9992
0.7 12707 1.5904
0.8 12535 1.5689
0.9 8106 1.0146
Total 798973

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 33727 4.2213
0.4 37131 4.6473
0.5 47546 5.9509
0.6 68881 8.6212
0.7 96225 12.0436
0.8 129524 16.2113
0.9 384677 48.1464
1.0 1262 0.1580
Total 798973

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 437413 72.1833
0.1 43125 7.1166
0.2 27956 4.6134
0.3 22486 3.7107
0.4 17349 2.8630
0.5 15918 2.6268
0.6 12669 2.0907
0.7 11188 1.8463
0.8 9877 1.6299
0.9 7994 1.3192
Total 605975

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 24437 4.0327
0.4 26700 4.4061
0.5 34626 5.7141
0.6 51751 8.5401
0.7 74083 12.2254
0.8 97733 16.1282
0.9 295812 48.8159
1.0 833 0.1375
Total 605975

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 398820 73.5714
0.1 38978 7.1904
0.2 26023 4.8005
0.3 18191 3.3557
0.4 15216 2.8069
0.5 11911 2.1973
0.6 10162 1.8746
0.7 9000 1.6603
0.8 8153 1.5040
0.9 5632 1.0389
Total 542086

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 22570 4.1635
0.4 25119 4.6338
0.5 32858 6.0614
0.6 48048 8.8635
0.7 65796 12.1376
0.8 87450 16.1321
0.9 259793 47.9247
1.0 452 0.0834
Total 542086

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 346716 73.1708
0.1 33034 6.9715
0.2 22327 4.7119
0.3 16930 3.5729
0.4 14674 3.0968
0.5 11408 2.4075
0.6 9079 1.9160
0.7 7903 1.6678
0.8 6452 1.3616
0.9 5322 1.1232
Total 473845

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 22696 4.7898
0.4 26129 5.5143
0.5 32770 6.9158
0.6 44965 9.4894
0.7 59486 12.5539
0.8 78168 16.4965
0.9 209187 44.1467
1.0 444 0.0937
Total 473845

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 391283 74.0225
0.1 37987 7.1863
0.2 23001 4.3513
0.3 18675 3.5329
0.4 14487 2.7406
0.5 12304 2.3277
0.6 10736 2.0310
0.7 9282 1.7560
0.8 6817 1.2896
0.9 4028 0.7620
Total 528600

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25521 4.8280
0.4 28407 5.3740
0.5 36272 6.8619
0.6 52212 9.8774
0.7 70134 13.2679
0.8 91440 17.2985
0.9 224220 42.4177
1.0 394 0.0745
Total 528600

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 331403 73.4966
0.1 30521 6.7688
0.2 23106 5.1243
0.3 15649 3.4705
0.4 13171 2.9210
0.5 11149 2.4726
0.6 8848 1.9623
0.7 8260 1.8319
0.8 5626 1.2477
0.9 3176 0.7044
Total 450909

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 23201 5.1454
0.4 26227 5.8165
0.5 35253 7.8182
0.6 47371 10.5057
0.7 60008 13.3082
0.8 75188 16.6748
0.9 183247 40.6395
1.0 414 0.0918
Total 450909

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 349861 72.9762
0.1 34521 7.2006
0.2 23289 4.8578
0.3 17632 3.6778
0.4 14135 2.9484
0.5 10703 2.2325
0.6 9769 2.0377
0.7 8042 1.6775
0.8 6556 1.3675
0.9 4910 1.0242
Total 479418

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 21172 4.4162
0.4 23905 4.9863
0.5 32032 6.6814
0.6 45169 9.4216
0.7 61073 12.7390
0.8 80345 16.7589
0.9 215252 44.8986
1.0 470 0.0980
Total 479418

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 268898 72.8186
0.1 29278 7.9286
0.2 18716 5.0684
0.3 13440 3.6396
0.4 9671 2.6189
0.5 8854 2.3977
0.6 6921 1.8742
0.7 6206 1.6806
0.8 4606 1.2473
0.9 2681 0.7260
Total 369271

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 19536 5.2904
0.4 23143 6.2672
0.5 28491 7.7155
0.6 38985 10.5573
0.7 48765 13.2057
0.8 61371 16.6195
0.9 148516 40.2187
1.0 464 0.1257
Total 369271

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 275060 73.3620
0.1 26908 7.1767
0.2 18260 4.8702
0.3 13519 3.6057
0.4 11255 3.0019
0.5 8611 2.2967
0.6 7984 2.1294
0.7 5788 1.5437
0.8 4644 1.2386
0.9 2906 0.7751
Total 374935

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17135 4.5701
0.4 19546 5.2132
0.5 25660 6.8439
0.6 36368 9.6998
0.7 47911 12.7785
0.8 62561 16.6858
0.9 165468 44.1324
1.0 286 0.0763
Total 374935

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 164578 72.1431
0.1 15793 6.9229
0.2 10467 4.5882
0.3 9211 4.0377
0.4 7017 3.0759
0.5 6138 2.6906
0.6 4857 2.1291
0.7 4436 1.9445
0.8 3999 1.7530
0.9 1631 0.7150
Total 228127

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 11221 4.9188
0.4 12180 5.3391
0.5 15789 6.9211
0.6 22363 9.8029
0.7 28610 12.5413
0.8 37684 16.5189
0.9 100073 43.8672
1.0 207 0.0907
Total 228127

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 159778 73.1075
0.1 15525 7.1036
0.2 10987 5.0272
0.3 7860 3.5964
0.4 6734 3.0812
0.5 5084 2.3262
0.6 4487 2.0531
0.7 4002 1.8311
0.8 2644 1.2098
0.9 1451 0.6639
Total 218552

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 11667 5.3383
0.4 13063 5.9771
0.5 16312 7.4637
0.6 21997 10.0649
0.7 28112 12.8628
0.8 35015 16.0214
0.9 92221 42.1964
1.0 165 0.0755
Total 218552

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 381183 74.5484
0.1 33241 6.5010
0.2 23714 4.6378
0.3 17803 3.4818
0.4 14055 2.7488
0.5 11854 2.3183
0.6 10555 2.0643
0.7 9557 1.8691
0.8 5662 1.1073
0.9 3699 0.7234
Total 511323

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 32981 6.4501
0.4 37441 7.3224
0.5 45846 8.9662
0.6 56486 11.0470
0.7 66874 13.0786
0.8 79206 15.4904
0.9 190810 37.3169
1.0 1679 0.3284
Total 511323

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering